import os
NOVA_HOME = '/home/projects/hornsteinlab/Collaboration/NOVA'
NOVA_DATA_HOME = '/home/projects/hornsteinlab/Collaboration/MOmaps'
LOGS_PATH = os.path.join(NOVA_HOME, "outputs", "preprocessing", "ManuscriptFinalData_80pct", "neuronsDay8", "logs")
PLOT_PATH = os.path.join(NOVA_HOME, 'outputs', 'preprocessing', 'ManuscriptFinalData_80pct', "neuronsDay8", 'QC_figures')
os.chdir(NOVA_HOME)
import pandas as pd
import contextlib
import io
from IPython.display import display, Javascript
from tools.preprocessing_tools.qc_reports.qc_utils import log_files_qc, run_validate_folder_structure, display_diff, sample_and_calc_variance, \
show_site_survival_dapi_brenner, show_site_survival_dapi_cellpose, \
show_site_survival_dapi_tiling, show_site_survival_target_brenner, \
calc_total_sums, plot_filtering_heatmap, show_total_sum_tables, \
plot_cell_count, plot_catplot, plot_hm_combine_batches, plot_hm, \
run_calc_hist_new
from tools.preprocessing_tools.qc_reports.qc_config import panels, markers, marker_info, cell_lines, cell_lines_to_cond,\
cell_lines_for_disp, reps, line_colors, lines_order, custom_palette,\
expected_dapi_raw
%load_ext autoreload
%autoreload 2
# choose batches
batches = [f'batch{i}' for i in range(5,10)]
batches
['batch5', 'batch6', 'batch7', 'batch8', 'batch9']
df = log_files_qc(LOGS_PATH, batches)
df_dapi = df[df.marker=='DAPI']
df_target = df[df.marker!='DAPI']
reading logs of batch8 reading logs of batch5 reading logs of batch6 reading logs of batch9 reading logs of batch7 Total of 5 files were read. Before dup handeling (296016, 21) After duplication removal #1: (296016, 22) After duplication removal #2: (296016, 22)
root_directory_raw = os.path.join(NOVA_DATA_HOME, 'input', 'images', 'raw', 'SpinningDisk')
batches_raw = [batch.replace("_16bit_no_downsample","") for batch in batches]
raws = run_validate_folder_structure(root_directory_raw, False, panels, markers,PLOT_PATH,marker_info,
cell_lines_to_cond, reps, cell_lines_for_disp, expected_dapi_raw,
batches=batches_raw)
batch5 Folder structure is valid. No bad files are found. Total Sites: 64800
======== batch6 Folder structure is valid. No bad files are found. Total Sites: 64800
======== batch7 Folder structure is valid. No bad files are found. Total Sites: 64800
======== batch8 Folder structure is valid. No bad files are found. Total Sites: 64800
======== batch9 Folder structure is valid. No bad files are found. Total Sites: 64800
======== ====================
root_directory_proc = os.path.join(NOVA_DATA_HOME, 'input', 'images', 'processed', 'ManuscriptFinalData_80pct',
'neuronsDay8')
procs = run_validate_folder_structure(root_directory_proc, True, panels, markers,PLOT_PATH,marker_info,
cell_lines_to_cond, reps, cell_lines_for_disp, expected_dapi_raw,
batches=batches)
batch5 Folder structure is invalid. Missing 11 paths: /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/FUSHomozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/TDP43/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/TBK1/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/WT/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/WT/stress/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/FUSRevertant/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/OPTN/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/FUSHeterozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/SCNA/Untreated/mitotracker /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/SCNA/Untreated/DCP1A /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch5/SCNA/Untreated/TIA1 No bad files are found. Total Sites: 48460
======== batch6 Folder structure is invalid. Missing 9 paths: /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/FUSHomozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/TDP43/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/TBK1/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/WT/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/WT/stress/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/FUSRevertant/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/OPTN/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/FUSHeterozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch6/SCNA/Untreated/TIA1 No bad files are found. Total Sites: 60739
======== batch7 Folder structure is invalid. Missing 9 paths: /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/FUSHomozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/TDP43/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/TBK1/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/WT/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/WT/stress/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/FUSRevertant/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/OPTN/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/FUSHeterozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch7/SCNA/Untreated/TIA1 No bad files are found. Total Sites: 61466
======== batch8 Folder structure is invalid. Missing 9 paths: /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/FUSHomozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/TDP43/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/TBK1/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/WT/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/WT/stress/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/FUSRevertant/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/OPTN/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/FUSHeterozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch8/SCNA/Untreated/TIA1 No bad files are found. Total Sites: 60957
======== batch9 Folder structure is invalid. Missing 9 paths: /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/FUSHomozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/TDP43/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/TBK1/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/WT/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/WT/stress/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/FUSRevertant/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/OPTN/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/FUSHeterozygous/Untreated/TIA1 /home/projects/hornsteinlab/Collaboration/MOmaps/input/images/processed/ManuscriptFinalData_80pct/neuronsDay8/batch9/SCNA/Untreated/TIA1 No bad files are found. Total Sites: 61080
======== ====================
display_diff(batches, raws, procs, PLOT_PATH)
batch5
======== batch6
======== batch7
======== batch8
======== batch9
========
for batch in batches:
with contextlib.redirect_stdout(io.StringIO()):
var = sample_and_calc_variance(root_directory_proc, batch,
sample_size_per_markers=200, num_markers=26)
print(f'{batch} var: ',var)
batch5 var: 0.014656935894448232 batch6 var: 0.016318794177940892 batch7 var: 0.015915956429535656 batch8 var: 0.016245487083204658 batch9 var: 0.01658928809417996
By order of filtering
Percentage out of the total sites
dapi_filter_by_brenner = show_site_survival_dapi_brenner(df_dapi,batches, line_colors, panels, reps)
Percentage out of the sites that passed the previous filter. In parenthesis are absolute values.
A site will be filtered out if Cellpose found 0 cells in it.
dapi_filter_by_cellpose = show_site_survival_dapi_cellpose(df_dapi, batches, dapi_filter_by_brenner, line_colors, panels, reps)
Percentage out of the sites that passed the previous filter. In parenthesis are absolute values.
A site will be filtered out if after tiling, no tile is containing at least one whole cell that Cellpose detected.
dapi_filter_by_tiling=show_site_survival_dapi_tiling(df_dapi, batches, dapi_filter_by_cellpose, line_colors, panels, reps)
Percentage out of the sites that passed the previous filter. In parenthesis are absolute values (if different than the percentages).
show_site_survival_target_brenner(df_dapi, df_target, dapi_filter_by_tiling, markers)
stats = ['n_valid_tiles','site_whole_cells_counts_sum','site_cell_count','site_cell_count_sum']
total_sum = calc_total_sums(df_target, df_dapi, stats, markers)
total_sum[~total_sum.marker.str.contains('TIA', regex=True)].n_valid_tiles.sum()
3213360
## Total tiles in wt lines
total_sum[(~total_sum.marker.str.contains('TIA', regex=True))&
(total_sum.cell_line_cond.isin(['WT stress', 'WT Untreated']))].n_valid_tiles.sum()
822738
## Total tiles in untreated lines
total_sum[(~total_sum.marker.str.contains('TIA', regex=True))&
((~total_sum.cell_line_cond.str.contains('WT')) | (total_sum.cell_line_cond=='WT Untreated'))].n_valid_tiles.sum()
2816265
total_sum[total_sum.marker =='DAPI'].site_whole_cells_counts_sum.sum()
689149.0
total_sum[total_sum.marker =='DAPI'].site_cell_count.sum()
1721557.0
total_sum[(total_sum.batch.str.contains('7|8', regex=True))
& (~total_sum.marker.str.contains('TIA1', regex=True))].n_valid_tiles.sum()
1296188
total_sum[(total_sum.batch.str.contains('7|8', regex=True))
& (total_sum.marker =='DAPI')].site_whole_cells_counts_sum.sum()
274468.0
show_total_sum_tables(total_sum)
| n_valid_tiles | % valid tiles | site_whole_cells_counts_sum | site_cell_count | |
|---|---|---|---|---|
| batch5 | ||||
| count | 620.000000 | 620.000000 | 620.000000 | 620.000000 |
| mean | 797.748387 | 7.977484 | 577.695161 | 1345.653226 |
| std | 532.103687 | 5.321037 | 390.174513 | 924.290458 |
| min | 1.000000 | 0.010000 | 1.000000 | 1.000000 |
| 25% | 284.750000 | 2.847500 | 205.750000 | 451.000000 |
| 50% | 852.500000 | 8.525000 | 598.000000 | 1434.000000 |
| 75% | 1252.000000 | 12.520000 | 902.000000 | 2108.000000 |
| max | 1715.000000 | 17.150000 | 1280.000000 | 2987.000000 |
| sum | 494604.000000 | NaN | 358171.000000 | 834305.000000 |
| expected_count | 450.000000 | 450.000000 | 450.000000 | 450.000000 |
| n_valid_tiles | % valid tiles | site_whole_cells_counts_sum | site_cell_count | |
|---|---|---|---|---|
| batch6 | ||||
| count | 627.000000 | 627.000000 | 627.000000 | 6.270000e+02 |
| mean | 1134.452951 | 11.344530 | 743.421053 | 1.957804e+03 |
| std | 286.694384 | 2.866944 | 193.942726 | 5.264662e+02 |
| min | 48.000000 | 0.480000 | 36.000000 | 8.400000e+01 |
| 25% | 930.500000 | 9.305000 | 612.000000 | 1.578000e+03 |
| 50% | 1169.000000 | 11.690000 | 755.000000 | 1.987000e+03 |
| 75% | 1332.000000 | 13.320000 | 863.000000 | 2.332000e+03 |
| max | 1669.000000 | 16.690000 | 1189.000000 | 2.993000e+03 |
| sum | 711302.000000 | NaN | 466125.000000 | 1.227543e+06 |
| expected_count | 450.000000 | 450.000000 | 450.000000 | 4.500000e+02 |
| n_valid_tiles | % valid tiles | site_whole_cells_counts_sum | site_cell_count | |
|---|---|---|---|---|
| batch7 | ||||
| count | 630.000000 | 630.000000 | 630.000000 | 6.300000e+02 |
| mean | 1050.255556 | 10.502556 | 715.953968 | 1.747508e+03 |
| std | 285.715774 | 2.857158 | 202.380671 | 5.070049e+02 |
| min | 206.000000 | 2.060000 | 137.000000 | 3.220000e+02 |
| 25% | 839.750000 | 8.397500 | 569.000000 | 1.393250e+03 |
| 50% | 1057.000000 | 10.570000 | 710.000000 | 1.765000e+03 |
| 75% | 1265.000000 | 12.650000 | 859.500000 | 2.129750e+03 |
| max | 1808.000000 | 18.080000 | 1259.000000 | 3.162000e+03 |
| sum | 661661.000000 | NaN | 451051.000000 | 1.100930e+06 |
| expected_count | 450.000000 | 450.000000 | 450.000000 | 4.500000e+02 |
| n_valid_tiles | % valid tiles | site_whole_cells_counts_sum | site_cell_count | |
|---|---|---|---|---|
| batch8 | ||||
| count | 629.000000 | 629.00000 | 629.000000 | 6.290000e+02 |
| mean | 1008.786963 | 10.08787 | 670.869634 | 1.691099e+03 |
| std | 277.006006 | 2.77006 | 187.150172 | 4.966986e+02 |
| min | 59.000000 | 0.59000 | 46.000000 | 9.100000e+01 |
| 25% | 836.000000 | 8.36000 | 546.000000 | 1.366000e+03 |
| 50% | 1002.000000 | 10.02000 | 663.000000 | 1.686000e+03 |
| 75% | 1199.000000 | 11.99000 | 801.000000 | 2.066000e+03 |
| max | 1731.000000 | 17.31000 | 1190.000000 | 2.996000e+03 |
| sum | 634527.000000 | NaN | 421977.000000 | 1.063701e+06 |
| expected_count | 450.000000 | 450.00000 | 450.000000 | 4.500000e+02 |
| n_valid_tiles | % valid tiles | site_whole_cells_counts_sum | site_cell_count | |
|---|---|---|---|---|
| batch9 | ||||
| count | 627.000000 | 627.000000 | 627.000000 | 6.270000e+02 |
| mean | 1134.395534 | 11.343955 | 753.824561 | 1.943244e+03 |
| std | 313.470280 | 3.134703 | 218.649641 | 5.661427e+02 |
| min | 154.000000 | 1.540000 | 97.000000 | 2.360000e+02 |
| 25% | 917.000000 | 9.170000 | 593.500000 | 1.519000e+03 |
| 50% | 1175.000000 | 11.750000 | 763.000000 | 2.038000e+03 |
| 75% | 1375.000000 | 13.750000 | 923.500000 | 2.368000e+03 |
| max | 1813.000000 | 18.130000 | 1323.000000 | 3.215000e+03 |
| sum | 711266.000000 | NaN | 472648.000000 | 1.218414e+06 |
| expected_count | 450.000000 | 450.000000 | 450.000000 | 4.500000e+02 |
| n valid tiles | % valid tiles | site_whole_cells_counts_sum | site_cell_count | |
|---|---|---|---|---|
| All batches | ||||
| count | 3.133000e+03 | 3133.000000 | 3.133000e+03 | 3.133000e+03 |
| mean | 1.025650e+03 | 10.256495 | 6.926179e+02 | 1.737917e+03 |
| std | 3.728328e+02 | 3.728328 | 2.578664e+02 | 6.621438e+02 |
| min | 1.000000e+00 | 0.010000 | 1.000000e+00 | 1.000000e+00 |
| 25% | 8.140000e+02 | 8.140000 | 5.450000e+02 | 1.349000e+03 |
| 50% | 1.057000e+03 | 10.570000 | 7.070000e+02 | 1.782000e+03 |
| 75% | 1.293000e+03 | 12.930000 | 8.620000e+02 | 2.225000e+03 |
| max | 1.813000e+03 | 18.130000 | 1.323000e+03 | 3.215000e+03 |
| sum | 3.213360e+06 | NaN | 2.169972e+06 | 5.444893e+06 |
| expected_count | 4.500000e+02 | 450.000000 | 4.500000e+02 | 4.500000e+02 |
For each batch, cell line, replicate and markerTotal number of tiles
to_heatmap = total_sum.rename(columns={'n_valid_tiles':'index'})
plot_filtering_heatmap(to_heatmap, extra_index='marker', vmin=None, vmax=None,
xlabel = 'Total number of tiles', show_sum=True, figsize=(6,8))
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
For each batch, cell line, replicate and markerTotal number of tiles
to_heatmap = total_sum.rename(columns={'site_whole_cells_counts_sum':'index'})
plot_filtering_heatmap(to_heatmap, extra_index='marker', vmin=None, vmax=None,
xlabel = 'Total number of whole cells', show_sum=True, figsize=(6,8))
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:381: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(ax.get_yticklabels(), fontsize=6)
df_no_empty_sites = df_dapi[df_dapi.n_valid_tiles !=0]
plot_cell_count(df_no_empty_sites, lines_order, custom_palette, y='site_cell_count_sum',
title='Cell Count Average per Site (from tiles)')
plot_cell_count(df_no_empty_sites, lines_order, custom_palette, y='site_whole_cells_counts_sum',
title='Whole Cell Count Average per Site')
plot_cell_count(df_no_empty_sites, lines_order, custom_palette, y='site_cell_count',
title='Cellpose Cell Count Average per Site')
df_dapi.groupby(['cell_line_cond']).n_valid_tiles.mean()
cell_line_cond FUSHeterozygous 7.278482 FUSHomozygous 12.740322 FUSRevertant 11.098691 OPTN 9.221037 SNCA 6.176806 TBK1 13.147027 TDP43 9.711553 WT Untreated 12.301475 WT stress 11.454986 Name: n_valid_tiles, dtype: float64
plot_catplot(df_dapi, custom_palette,reps, x='n_valid_tiles', x_title='valid tiles count', batch_min=4, batch_max=9)
/home/projects/hornsteinlab/Collaboration/NOVA/tools/preprocessing_tools/qc_reports/qc_utils.py:1017: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy df.loc[:, 'batch_rep'] = df['batch'] + " " + df['rep']
plot_hm(df_dapi, split_by='rep', rows='cell_line', columns='panel', vmax=3)
df_dapi[['cells_count_in_valid_tiles_mean']].mean()
cells_count_in_valid_tiles_mean 1.43989 dtype: float64
df_dapi[['site_cell_count']].mean()
site_cell_count 17.489455 dtype: float64
## Only batches 7&8
plot_hm_combine_batches(df_dapi, batches=['batch7','batch8'],
reps = ['rep1','rep2'],rows='cell_line', columns='panel', vmax=3)
for batch in batches:
print(batch)
#batch_num = batch.replace('batch',"")
run_calc_hist_new(batch,cell_lines_for_disp, markers, root_directory_raw, root_directory_proc,
hist_sample=10,sample_size_per_markers=200, ncols=7, nrows=4)
print("="*30)
# save notebook as HTML ( the HTML will be saved in the same folder the original script is)
display(Javascript('IPython.notebook.save_checkpoint();'))
os.system(f'jupyter nbconvert --to html tools/preprocessing_tools/qc_reports/qc_report_d8.ipynb --output {NOVA_HOME}/manuscript/preprocessing_qc_reports/qc_report_d8.html')